Contacts of the helix formed by residues 15 - 27 (chain C) in PDB entry 1ZMC
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 15 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13C GLY 3.4 4.9 + - - -
14C SER* 1.3 79.8 - - - +
16C PRO* 1.3 74.8 - - - +
17C GLY 3.0 3.5 + - - -
18C GLY 3.1 1.1 + - - +
19C TYR* 2.9 24.0 + - - -
42C GLY 4.4 0.2 - - - -
43C GLY 3.6 8.1 - - - -
480C FAD 3.2 27.3 + - - -
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Residues in contact with PRO 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C GLY* 1.3 82.3 - - - +
17C GLY* 1.3 57.2 + - - +
19C TYR* 3.9 11.0 - - + -
20C VAL* 3.1 17.8 - - - +
42C GLY 4.0 8.2 - - - +
45C CYS* 3.5 21.3 - - + -
328C ALA* 3.8 22.2 - - + +
332C GLU* 2.9 36.6 - - + +
480C FAD 3.1 43.5 - - - +
452D HIS* 5.6 0.4 - - + +
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Residues in contact with GLY 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C PRO* 1.3 78.6 - - - +
18C GLY* 1.3 59.9 + - - +
20C VAL* 3.5 1.4 + - - +
21C ALA* 2.9 31.2 + - - +
147C ALA* 5.1 0.2 - - - -
318C ILE* 3.6 14.0 - - - +
331C ALA* 3.4 30.0 - - - +
332C GLU* 4.0 1.1 - - - -
335C GLY* 4.2 1.6 - - - -
480C FAD 3.0 11.5 + - - -
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Residues in contact with GLY 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C VAL* 3.6 9.0 - - - +
13C GLY 3.2 22.7 - - - -
15C GLY 3.1 4.6 + - - -
17C GLY* 1.3 76.0 - - - +
19C TYR* 1.3 52.1 + - - +
21C ALA* 3.1 4.1 + - - +
22C ALA* 2.7 36.7 + - - +
34C CYS* 4.9 0.4 - - - -
147C ALA* 3.6 22.3 - - - +
480C FAD 4.0 0.8 + - - -
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Residues in contact with TYR 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C GLY 3.9 3.0 + - - -
14C SER* 3.6 12.6 - - - +
15C GLY 2.9 30.4 + - - +
16C PRO* 3.9 11.2 - - + -
18C GLY* 1.3 73.4 - - - -
20C VAL* 1.3 77.5 + - + +
22C ALA 3.9 0.2 - - - -
23C ILE* 3.1 53.0 + - + +
42C GLY* 5.0 0.9 - - - -
103C ILE* 3.8 45.0 - - + +
106C LEU* 4.6 2.2 - - + -
107C PHE* 3.6 24.0 - + + -
332C GLU* 4.7 6.4 + - - -
392D SER* 5.6 1.9 + - - -
452D HIS* 5.8 3.1 - - - -
472D ILE* 4.9 0.2 - - + -
473D ASN* 2.6 32.9 + - - -
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Residues in contact with VAL 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C PRO 3.1 24.1 + - - +
17C GLY 3.5 2.6 + - - +
18C GLY 3.2 0.4 - - - -
19C TYR* 1.3 97.1 - - + +
21C ALA* 1.3 61.5 + - - +
23C ILE* 3.9 1.0 - - - +
24C LYS* 3.0 28.1 + - - +
332C GLU* 3.7 34.3 - - + +
336C ILE* 3.4 34.5 - - + -
472D ILE* 4.1 21.9 - - + +
473D ASN* 5.4 1.3 - - - +
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Residues in contact with ALA 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C VAL* 4.5 0.9 - - + -
17C GLY 2.9 21.0 + - - +
18C GLY 3.3 5.2 - - - +
20C VAL* 1.3 75.5 - - - +
22C ALA* 1.3 55.7 + - - +
24C LYS* 3.3 2.1 + - - -
25C ALA* 2.8 36.7 + - - +
145C LEU* 3.5 30.7 - - + -
335C GLY* 4.0 21.3 - - - +
336C ILE 4.7 0.2 - - - +
339C VAL* 3.4 11.0 - - + +
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Residues in contact with ALA 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C VAL* 4.1 10.7 - - + +
18C GLY 2.7 20.3 + - - +
19C TYR 3.9 4.7 - - - +
21C ALA* 1.3 71.3 - - - +
23C ILE* 1.3 64.6 + - - +
25C ALA* 2.9 13.2 + - - +
26C ALA* 3.0 13.3 + - - +
32C THR* 3.7 27.1 - - + +
34C CYS* 4.2 9.4 - - + -
107C PHE* 4.0 20.0 - - + -
112C VAL* 4.2 5.4 - - + -
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Residues in contact with ILE 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C TYR* 3.1 43.4 + - + +
20C VAL 3.9 3.1 - - - +
22C ALA* 1.3 77.1 - - - +
24C LYS* 1.3 63.9 + - - +
26C ALA* 3.2 4.9 + - - +
27C GLN* 3.1 40.7 + - - +
106C LEU* 3.9 23.6 - - + +
107C PHE* 3.9 16.4 - - + -
110C ASN* 3.7 23.4 - - - +
112C VAL* 4.3 8.7 - - + +
472D ILE* 3.9 30.7 - - + +
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Residues in contact with LYS 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C VAL 3.0 20.0 + - - +
21C ALA 3.9 2.5 - - - +
23C ILE* 1.3 77.0 - - - +
25C ALA* 1.3 59.3 + - - +
27C GLN* 3.6 17.3 + - - +
28C LEU* 3.0 47.4 + - + +
336C ILE* 3.7 38.4 - - + +
339C VAL* 3.9 13.5 - - + -
340C GLU* 4.0 20.0 + - - +
464D LEU* 4.6 12.8 - - - +
468D PHE* 3.8 38.7 - - + -
472D ILE* 4.0 10.3 - - + -
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Residues in contact with ALA 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C VAL* 4.3 11.0 - - + -
21C ALA 2.8 14.4 + - - +
22C ALA* 3.1 11.4 - - - +
24C LYS* 1.3 74.3 - - - +
26C ALA* 1.3 65.5 - - - +
28C LEU* 3.1 9.5 + - - +
30C PHE* 3.3 27.3 + - + +
32C THR* 3.4 19.5 - - + +
339C VAL* 3.3 24.7 - - + +
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Residues in contact with ALA 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C ALA 3.0 5.8 + - - +
23C ILE 3.2 6.9 + - - +
25C ALA* 1.3 76.9 - - - +
27C GLN* 1.3 61.3 + - - +
28C LEU 3.1 0.2 - - - -
29C GLY* 3.2 13.5 + - - -
30C PHE 3.6 16.4 + - - +
32C THR* 3.4 7.3 + - - +
110C ASN* 3.3 29.3 - - + +
111C LYS 5.1 1.8 - - - +
112C VAL* 3.8 19.5 - - + +
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Residues in contact with GLN 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C ILE* 3.1 30.7 + - - +
24C LYS* 3.9 22.0 - - - +
25C ALA 3.2 0.2 - - - -
26C ALA* 1.3 76.1 - - - +
28C LEU* 1.3 60.0 + - - +
29C GLY 3.4 0.2 - - - -
109C GLN* 5.8 0.8 - - - +
110C ASN* 3.4 26.1 + - - +
464D LEU* 6.1 0.2 - - - +
468D PHE* 3.7 33.9 - - + -
470D LYS* 3.6 37.4 + - + +
471D SER 3.0 25.5 + - - +
472D ILE* 4.1 5.9 - - - +
474D PHE* 5.5 0.4 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il